With the large number of genome sequencing projects completed or underway, a new avenue for finding such candidate regions is rapidly becoming available. Namely, from orthologous sequences collected from a (large) number of species, identify those regions that are best conserved. We have already developed one specialized algorithm that performs such "phylogenetic footprinting" to identify potential regulatory elements in nucleotide sequences. This algorithm will be both applied to the discovery of novel regulatory elements and extended along multiple axes: 1. Phylogenetic footprinting algorithms will be applied to discover novel regulatory elements in orthologous nucleotide sequences. 2. Phylogenetic footprinting algorithms will be applied to discover novel functional motifs in orthologous protein sequences. 3. Algorithms to discover secondary structure motifs in orthologous RNA molecules will be developed. 4. Algorithms that identify exons from syntenic genomic sequences of multiple species will be developed.